


Millenium puzzle wish- Matters of the soul

by ryuukko



Category: Yu-Gi-Oh!
Genre: Duel Monsters, Fluff, Hurt/Comfort, M/M, NSFW, NSFW in later chapters, Post-Series, Reunion, Yugi is in college now, not actually sad
Language: English
Status: Completed
Published: 2017-02-24
Updated: 2017-02-24
Packaged: 2018-09-26 15:09:29
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 2,643
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/9908135
Author URL: https://archiveofourown.org/users/ryuukko/pseuds/ryuukko
Summary: After Atem left, Yugi tries to move on. Doesn't work.What's the next step? Go SOUL searching for his SOUL Mate.





	1. Chapter 1

It had been a few years since Yami left. Yugi Moto was now in college. Being a freshman again sucked. He wasn't a pipsqueak anymore, but being apart of the new batch of students exposed him to weird stuff. People experimenting, starting rumors, and gossiping faster than you could say second semester.  
He sat in class, ignoring quizzed gazes. Yes, he was the duelist champion, he had gotten about a hundred questions about his hair, but the thing that bothered him the most were the inquiries of the puzzle.

'That looks expensive you can probably get thousands for it on eBay!'

'Can I borrow it? I wanna see how heavy it is!'

'Can I buy that from you?'

Yugi managed to develop a bad reputation quickly among his new peers. The bubbly, friendly duelist didn't have the patience for people getting near his most prized possession. They had no understanding of its story, it's personal value. Once, it carried another soul. One that Yugi bonded with on a level that could not be matched. He felt the emptiness bore into him, with each step the Pharaoh took away from him, the deeper it got. His words echoed in his head from the second tournament-

'I want to be with you forever.'

The college student gripped the chain of the puzzle. It wasn't fair to beg Atem to stay. His soul needed to rest. He may have died a young pharaoh, but had lived enough to last a lifetime. Yugi told himself he'd get over it and move on. His work would occupy his time and mind.But it never did. Not enough to keep the past in the past.

He worked summer and school year, saving up money to go to Egypt. He had to see his soul mate one last time.

In his second year, he was able to depart for the famed pyramids. His classmates thought he was crazy. Times have changed, safety was not guaranteed. No matter. Yugi placed his bag in the overhead bin, plugged in his music, and closed his eyes.

\----

City lights glowed under the twinkling stars, the city reminded him a lot of home. The warm night air rushed past Yugi's face as he made his way to the airport hotel. The minute he stepped in his room, he plopped right on his bed and fell asleep in his clothes.  
\---  
Checking his phone first thing in the morning was a habit he developed during college. Weather, email, boring stuff. Back during his early to mid high school days, he'd look up and see his other half floating around his room. Yugi would go through his boring routine happily, discussing things with the ancient spirit. Answering questions about the present day was a favorite topic. They would take turns explaining topics from their educations. Traditions, mannerisms, differences in culture, it all woke Yugi up with a fresh look at the new day.

Now the shrill alarm from his smart phone greeted him to the new day. Just like millions of others around the world.

Reaching for the side button, he yawned and stretched. Today was the day. At long last, the dawn that he had worked so hard for.

Yugi's determination got him this far, no use in turning back now. Even if it was 113°F.

He wiped his arm across his forehead, he was doing this. How people wore layers upon layers of clothing under the hot Egyptian sun without Immediately passing out remained more mysterious than the ancient secrets of the past. Perhaps it was one of them.

Yugi had to make a choice. Halfway there, he had to either leave the team behind, or run the risk of bringing them to a haunted, cursed tomb that could ultimately kill them all. Sure, Atem's spirit was at rest, but who knows would could still be lingering around. Yugi could die alone...what if he wasn't welcomed there? What if Atem actually sees him?

The ex-duelist bit his lip. He had to go alone.

\---  
He shivered, stepping into the uncomfortably hot entrance. On the outside, the walls were as plain as could be. It was not until one arrived into the deepest chamber that the beautiful depictions and writings appeared. As he descended, Yugi sighed in relief. Cool, shaded areas replaced the sun-beaten pathway. The stairs led to a first chamber, which once held traps. Like I'm the movies, there actually was a body there. Yugi's seen unbelievably scary things, but that takes the cake. Maybe it was because he was all alone. No Joey, no Tèa, no Tristan, not even Kaiba.

Unlike the last time he had flown here, walking to Atem's chamber required actual walking. Having his growth spurt kick in at high gear meant that he was now ducking under the smaller passageways. Being 5 foot 8 now didn't seem so great. The worst part was having to crawl through the last connection. He had to leave his torch behind.

It was then that he heard crumbling. His heart stopped.

'No....'

The next one was slightly louder.

'Nonono! Please-'

Yugi held his breath and screwed his eyes shut. This was where he was going to die. With memorial flowers in his bag. How ironic.

He then opened his eyes, expecting darkness. Instead, he saw a shimmering golden glow ahead of him. Under a stone tablet on the wall. He did not realize it was his puzzle that had teleported, chain and all, to Yami's grave. He shimmied his way out of the narrow passage way and approaches it.

Taking the flowers from his bag, he kneels in front of it. "H-hi...it's me..."

'That was a stupid thing to say. What are you? 14?' He thought to himself. Yugi cleared his thoat. "I know I promised I would let you go but...I can't...I mean I will! You totally deserve to be with all of your family and friends after everything you've done for all of us. 5000 long years you sat alone in this tomb...I can't even go five years without missing your presence. Pathetic, huh?" He let out a chuckle. "I hope you are doing well and I just came by to say thank you. Thank you for granting my wish...You not only manage to grant it, but you filled me with hope and courage. And a bond that I'll never forget for as long as I lived. I miss feeling your soul so close to mine...."

Yugi wiped his face and placed the flowers down on the sarcophagus. "I came hear to say goodbye. For real this time. There was something I just couldn't say in front of everyone, because it would have made things way more complex...."

The puzzle glowed brighter, and floated in the air. Yugi's eyes were shut, holding back tears. The light stretched into the shape of a human body, about five feet or so. A figure dropped to his knees and carefully placed a hand on Yugi's shoulder.

"And what would that be, Yugi?"

Yugi froze. That voice....

"Atem?"

Through the darkness, Yugi gazed into an ancient ruby gaze he thought he had lost forever. In his Pharaoh clothes, he smiles and takes his hand. A golden glow radiates from his jewelry. Just enough so that Yugi could see him. The sight was simply breathtaking. Yugi reached up to touch his cheek. It wasn't cold, it wasn't dead. The Pharaoh was a living and breathing human being again.

"These flowers are wonderful."

"O-oh! I'm sorry they got a little crushed!"

Yami chuckled, squeezing Yugi's hand slightly.

"I think I know why you're here."

"Wha-what do you me-" he squealed slightly when a soft pair of lips were on his own. A thousand things ran though his mind. How was this all happening? What was he going to do when he left? Why was his other half not betrayed by his return?

Atem pulled back. The Pharaoh couldn't hear the younger man's thoughts anymore, but he could sense them.

"I'm sorry Yugi...was I mistaken in your wishes?" He asked almost nervously.

"N-no! I love you Atem!" He hugged him and began to sob. "It's just-...just...."

"I have returned. I will never leave you again." He hugged back and pulled him close. "I will miss all of my past, but it does not compare to you. We are bonded Yugi. Besides, nothing is the same. I feel as though you are really the other half of my soul. I feel all of the love and protection you had for the puzzle too. After many nights, my court has decided that it is best if I return to you. One's afterlife requires a full soul."

"Wait...so you got kicked out of heaven because of me?" Yugi was horrified.

"No! Oh Ra no....my afterlife is being with you. You complete me Yugi." He ran a hand through his hair. "I wish to stay by your side, silly."

Yugi smiled and kissed him again. Yami couldn't help but moan softly. The younger one was glad it was dark, Yami couldn't see his Redding face.

\---  
Tbc!  
Next chapter should be up in a few days.


	2. Can't take the heat, get out of the blazing sun

**Summary for the Chapter:**

> Okay I admit it I haven't watched the last EP bc I don't wanna cry fite me this is an au

"A-atem.." Yugi gasped and clung to the other. "I thought you would be upset with me coming back. The duel was supposed to seperate us forever, and yet, I can't get you out of my head."

The two remained in a kneeling position for a good couple of minutes. Yami rubbed his soulmate's back, attempting to comfort him. A warm smile greeted Yugi when he finally picked his head up. 

"So Aibou, where do we go from here?"

Yugi blinked and then drew himself to his full height. Yami was caught off guard and murmured something in his native language. The sharp features of his face molded into surprise. He took Yugi's hand and was mystified. 

"What? Oh...yeah it's been a while. I sort of..grew a bit.." Yugi blushed. "Who knows..maybe you'll have a growth spurt too?" 

That lopsided smile nearly melted Atem's kneels beating heart. He took Yugi's hand and followed him to the crawl space. Yugi gasped when the area began to crumble in front of him. He had to move fast. The college student pulled his other half through the hole and carried him on his back. "Hold on!"

He made a mad dash for the exit, the next thing he knew, Yugi was in a dreamless sleep.  
\----

Sunlight, real sunlight. It felt good to be back. Even if it was way too hot on this particular day. Yami drew himself up to his knees and looked down. "Aibou, your quick thinking saved us!...Aibou?"

He got off of him, reached for his arm and turned him over. The boy was unconscious. Scanning the vast land, there was no life in sight. No one that could aid them. If this were 5000 years ago, he would whisk him back to the palace. They would have been safe there. Now, nothing remains, except for remains. The memories of his ancient peoples. He covered Yugi with his cape and sighed. What were they going to do? If he managed to get him into a town, he couldn't go around wearing the attire he was without attracting unwanted attention. But he had to do something.

 

"My Pharaoh!"

Ishizu?

"Quickly, come with us."

Marik jumped off of his camel and picked up Yugi. 

\---

Amethyst eyes slowly revealed themselves. They were met with passionate red ones. His hand was encased in a gentle hold. A pulse, that was what brought Yugi to. Not his own, but Yami's. 

"How...?"

"You were saved by a letter Yugi."

"Huh?"

"The Ishtar family got word that you were traveling to the ruins. The side that wasn't destroyed. Even though their duty was carried out, they came back just in time."

"Wait what? Slow down I feel..."

"Ah..right..." he planted a kiss on his forehead. "Rest, my sweet partner. I will return when you awaken." 

And with that, Yugi returned to a dreamless slumber.


	3. Chapter 3

**Summary for the Chapter:**

> Yugi recovers from fainting, Atem sees some familiar faces in the meantime.

"He came all this way...for me.." Atem brushed his bangs from his face. Gold adorned his body, brought from ancient times. He appeared as though he just walked out of his throne room. 

What had Yugi been up to after his departure? He still had a lot to learn about the modern world. Although he kept many of his memories from the time he spent sharing his partner's body, Atem found himself at a loss for what people did after high school. Did they work? Was there some sort of higher learning? Did people roam free, searching for their own destinies? 

Questions swirled in his mind like a raging sandstorm. He couldn't wait for Yugi to wake up.

'My pharaoh...'

Yami blinked. That couldn't be who he thought it was....

He looked over to Yugi's bag. A glow radiated underneath the thin yet dutiable fabric. Taking a glance at his unconscious companion, he had second thoughts about investigating. The glow was in the shape of a square. Could it be the heart of the cards calling out to him?

He reached over slowly and extracted the clear case from the inner pocket of the bag and gazed upon an old friend. The Dark Magician. Atem cautiously took the card out and held it with the most gentle grasp he could manage. A pang of emotion swept over him, yet his expression remained calm. He took a moment to remember his fallen friend, whom was forever trapped in stone. 

'I see that your cross into this world was successful. It is good to see you again.'

Ruby eyes snapped open. Something tall and purple floated in front of him. The white flooring and blandly decorated wall was still visible behind the figure. 

"Mahad?" Yami asked.

He received a smile and a nod. "You see, you visited the world of your memories. You witnessed what became of me. I was not able to join you and the others in the afterlife."

"So you've been trapped in stone all of this time?"

"Not exactly."

"What do you mean by that?"

Mahad picked up the deck and smiled. "There are times when your other half would pickup his deck and speak to it. I know that three monsters spirits inhabit it other than times when he duels. Kuriboh, my apprentice, and myself."

"Ah, dark magician girl...how is she?"

"Why don't you ask her yourself?" 

Atem took the deck, and looked down at it with an inquisitive eyebrow. Mahad had shown up on his own, so would Dark Magician girl show up as well-

"Hello pharaoh!"

Atem jumped in his seat. She had snuck upon him! Just like an old friend of his....

"Ugh! You were out in the desert without a hat again!"

"Mana?!"

"Mhmm!"

"What are you doing here?"

"Why I merged with my ka!"

"Huh?"

"Yeah, we're really close, remember? If you were coming to this world, I would too and wait for you!" Mana stated proudly. "Don't worry, I left Seto with a court Magician."

The pharaoh smiled warmly and chuckled.

Mahad couldn't help but smile too; but it didn't last long. He looked over to Yugi and saw an all too familiar state of distress lightly covering his unconscious features. Many a nights the young one had dozed off at his desk holding his favorite card. Mahad could only watch as Yugi's soul cried out for it's other half. Night after night, this went on. Mana floated to him and frowned. 

"Poor thing. He must think that retrieving you from the tomb was a dream, and nothing more." She sighed.

Atem gasped lightly and took Yugi's hand. He kisses the knuckles and then his palm. 'Wake up!' He mentally pleaded. 'Aibou, return to me soon!'


End file.
